Dataset Information

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma.

ABSTRACT: Existing studies characterizing gut microbiome variation in the United States suffer from population ascertainment biases, with individuals of American Indian ancestry being among the most underrepresented. Here, we describe the first gut microbiome diversity study of an American Indian community. We partnered with the Cheyenne and Arapaho (C&A), federally recognized American Indian tribes in Oklahoma, and compared gut microbiome diversity and metabolic function of C&A participants to individuals of non-native ancestry in Oklahoma (NNIs). While the C&A and NNI participants share microbiome features common to industrialized populations, the C&A participants had taxonomic profiles characterized by a reduced abundance of the anti-inflammatory bacterial genus Faecalibacterium, along with a fecal metabolite profile similar to dysbiotic states described for metabolic disorders. American Indians are known to be at elevated risk for metabolic disorders. While many aspects of this health disparity remain poorly understood, our results support the need to further study the microbiome as a contributing factor. As the field of microbiome research transitions to therapeutic interventions, it raises concerns that the continued exclusion and lack of participation of American Indian communities in these studies will further exacerbate health disparities. To increase momentum in fostering these much needed partnerships, it is essential that the scientific community actively engage in and recruit these vulnerable populations in basic research through a strategy that promotes mutual trust and understanding, as outlined in this study.

SUBMITTER: Sankaranarayanan K

PROVIDER: S-EPMC4703035 | biostudies-literature | 2015 Dec

REPOSITORIES: biostudies-literature

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Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma.

Sankaranarayanan Krithivasan K Ozga Andrew T AT Warinner Christina C Tito Raul Y RY Obregon-Tito Alexandra J AJ Xu Jiawu J Gaffney Patrick M PM Jervis Lori L LL Cox Derrell D Stephens Lancer L Foster Morris M Tallbull Gloria G Spicer Paul P Lewis Cecil M CM

Current biology : CB 20151206 24

Existing studies characterizing gut microbiome variation in the United States suffer from population ascertainment biases, with individuals of American Indian ancestry being among the most underrepresented. Here, we describe the first gut microbiome diversity study of an American Indian community. We partnered with the Cheyenne and Arapaho (C&A), federally recognized American Indian tribes in Oklahoma, and compared gut microbiome diversity and metabolic function of C&A participants to individual ...[more]

PMID: 26671671

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Project description:Objective: The gut microecosystem is the largest microecosystem in the human body and has been proven to be linked to neurological diseases. The main objective of this study was to characterize the fecal microbiome, investigate the differences between epilepsy patients and healthy controls, and evaluate the potential efficacy of the fecal microbiome as a diagnostic tool for epilepsy. Design: We collected 74 fecal samples from epilepsy patients (Eps, n = 24) and healthy controls (HCs, n = 50) in the First Affiliated Hospital of Zhengzhou University and subjected the samples to 16S rRNA MiSeq sequencing and analysis. We set up a train set and a test set, identified the optimal microbial markers for epilepsy after characterizing the gut microbiome in the former and built a diagnostic model, then validated it in the validation group. Results: There were significant differences in microbial communities between the two groups. The α-diversity of the HCs was higher than that of the epilepsy group, but the Venn diagram showed that there were more unique operational taxonomic unit (OTU) in the epilepsy group. At the phylum level, Proteobacteria and Actinobacteriota increased significantly in Eps, while the relative abundance of Bacteroidota increased in HCs. Compared with HCs, Eps were enriched in 23 genera, including Faecalibacterium, Escherichia-Shigella, Subdoligranulum and Enterobacteriaceae-unclassified. In contrast, 59 genera including Bacteroides, Megamonas, Prevotella, Lachnospiraceae-unclassified and Blautia increased in the HCs. In Spearman correlation analysis, age, WBC, RBC, PLT, ALB, CREA, TBIL, Hb and Urea were positively correlated with most of the different OTUs. Seizure-type, course and frequency are negatively correlated with most of the different OTUs. In addition, twenty-two optimal microbial markers were identified by a fivefold cross-validation of the random forest model. In the established train set and test set, the area under the curve was 0.9771 and 0.993, respectively. Conclusion: Our study was the first to characterize the gut microbiome of Eps and HCs in central China and demonstrate the potential efficacy of microbial markers as a noninvasive biological diagnostic tool for epilepsy.

Project description:Archaea are habitual residents of the human gut flora but are detected at substantially lower frequencies than bacteria. Previous studies have indicated that each human harbors very few archaeal species. However, the low diversity of human-associated archaea that has been detected could be due to the preponderance of bacteria in these communities, such that relatively few sequences are classified as Archaea even when microbiomes are sampled deeply. Moreover, the universal prokaryotic primer pair typically used to interrogate microbial diversity has low specificity to the archaeal domain, potentially leaving vast amounts of diversity unobserved. As a result, the prevalence, diversity, and distribution of archaea may be substantially underestimated. Here we evaluate archaeal diversity in gut microbiomes using an approach that targets virtually all known members of this domain. Comparing microbiomes across five great ape species allowed us to examine the dynamics of archaeal lineages over evolutionary time scales. These analyses revealed hundreds of gut-associated archaeal lineages, indicating that upwards of 90% of the archaeal diversity in the human and great ape gut microbiomes has been overlooked. Additionally, these results indicate a progressive reduction in archaeal diversity in the human lineage, paralleling the decline reported for bacteria. IMPORTANCE Our findings show that Archaea are a habitual and vital component of human and great ape gut microbiomes but are largely ignored on account of the failure of previous studies to realize their full diversity. Here we report unprecedented levels of archaeal diversity in great ape gut microbiomes, exceeding that detected by conventional 16S rRNA gene surveys. Paralleling what has been reported for bacteria, there is a vast reduction of archaeal diversity in humans. Our study demonstrates that archaeal diversity in the great ape gut microbiome greatly exceeds that reported previously and provides the basis for further studies on the role of archaea in the gut microbiome.

Dataset Information

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma.

Publications

Gut Microbiome Diversity among Cheyenne and Arapaho Individuals from Western Oklahoma.

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